Yesterday the FAA sought $10.2 million in civil damages from Southwest Airlines for neglecting to inspect the fuselages of 46 of its planes. In documents the FAA submitted to Congress, it alleges “the airline flew at least 117 of its planes in violation of mandatory safety checks” over a 30 month period. Southwest says its passengers were never in danger, and that it was an honest oversight that they caught on their own and revealed to the FAA—but (here’s where it gets interesting) an FAA inspector has testified that Southwest continued to fly a plane after he discovered the failed inspections and notified them. Now the U.S. Department of Transportation and Congress are asking why the FAA didn’t ground the planes as soon as they knew about the missed inspections, and a couple of FAA whistleblowers are leaking internal docs to the press. Only after the issue became public knowledge did the FAA seek civil damages.

The [whistleblower] inspectors say FAA managers knew about the lapse in safety at Southwest, but decided to allow the airline to conduct the safety checks on a slower schedule because taking “aircraft out of service would have disrupted Southwest Airlines’ flight schedule.”

According to statements made by one of the FAA inspectors seeking whistle-blower status, a manager at the FAA “permitted the operation of these unsafe aircraft in a matter that would provide relief” to the airline, even though customers were on board.

Laura Brown, an FAA spokeswoman, told CNN that the administration has taken action and that a supervisor who was in charge of overseeing Southwest is “no longer in a supervisory position.”

Here’s Southwest’s response to the civil penalty news:

“The FAA penalty is related to one of many routine and redundant inspections on our aircraft fleet involving an extremely small area in one of the many overlapping inspections. These inspections were designed to detect early signs of skin cracking,” the airline said in a statement Thursday evening.

“Southwest Airlines discovered the missed inspection area, disclosed it to the FAA, and promptly reinspected all potentially affected aircraft in March 2007. The FAA approved our actions and considered the matter closed as of April 2007.”

According to CNN, “the safety inspections ignored or delayed by the airline were mandated after two fatal crashes and one fatal incident, all involving Boeing’s 737, the only type of airplane Southwest flies.”